Supported input
Pankegg was developed to integrate output files from a variety of metagenomics tools, such as CheckM2, Sourmash, GTDB-TK and EggNOG. You can combine them all, or only add the ones that are interesting for you.
Input files
| Tool | Input File | Data Extracted |
|---|---|---|
| checkm2 | quality_report.tsv | bin completeness and contamination |
| Sourmash | *.txt | ID, Status and Taxonomic classification |
| GTDB-TK | *.summary.tsv | User genome and Taxonomic classification |
| EggNOG | *.annotations.tsv | KEGG Orthologs, KEGG Pathways, GO terms, Description |
Additional Input Files Provided by Pankegg
PANKEGG requires more input files. However, these are already provided and you don’t need to worry about them. They are located in the data directory.
| File Name | Description | Data Origin |
|---|---|---|
| kegg_map_info.tsv | Contains mapID, pathway name, and total number of orthologs per pathway (map) | Extracted from KEGG pathway database |
| kegg_map_orthologs.tsv | Contains mapID, pathway name, and list of orthologs per pathway (map) | Extracted from KEGG pathway database |
| ko.txt | Contains the IDs and names of orthologs | Extracted from KEGG orthologs database |
| pathway.txt | Contains map IDs (pathways) and their names | Extracted from KEGG pathway database |
| pathway_groups.txt | Maps IDs grouped by KEGG sub-categories | Extracted from KEGG pathway database |